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Germonline

Description

The GermOnline 4.0 gateway is a cross-species microarray expression database focusing on germline development, meiosis and gametogenesis as well as the mitotic cell cycle. (created in 2009).

Access conditions

Free access

No website documented

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Staphylococcal regulatory RNAs

Description

The ‘Staphylococcal Regulatory RNA Database’ compiled all published data in a single interface including genetic locations, sequences and other features. SRD proposes a simplified and unified identifier for Staphylococcal regulatory RNAs (srn) based on the sRNA’s genetic location in S. aureus strain N315 which served as a reference.

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Dog CNV database

Description

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4

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ReproGenomics Viewer

Description

The ReproGenomics Viewer (RGV) is a cross-species genomic toolbox for the reproductive community. The system is based on the implementation of a JBrowse genome browser and a Galaxy bioinformatics workflow environment.

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BioMAJ2Galaxy

Description

BioMAJ2Galaxy makes it possible to configure BioMAJ to automatically download some reference data, to then convert them and/or index it in various formats, and then make this data available in a Galaxy server using data libraries or data managers.

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GO-Docker

Description

It is a cluster management tool using Docker as execution/isolation system. The software does not manage however itself the dispatch of the commands on the remote nodes. For this, it integrates with container management tools (Docker Swarm, Apache Mesos, ...)

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BioShaDock

Description

BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts deﬁned in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user deﬁned tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists.

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PepPSY

Description

PepPSy has been developed as a user-friendly gene expression-based prioritization system, to help investigators to determine in which human tissues they should look for an unseen protein and curators to quickly look at available transcriptomics/proteomics data for a list of proteins.

GO2Pub

Description

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Autograph

Description

AutoGRAPH is an integrated web server for multi-species comparative genomic analysis. It is designed for constructing and visualizing synteny maps between two or three species, determination and display of macrosynteny and microsynteny relationships among species, and for highlighting evolutionary breakpoints.

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Protomata

Description

Given a sample of (unaligned) sequences belonging to a structural or functional family of proteins, Protomata-Learner infers automata characterizing the family. Automata are graphical models representing a (potentially infinite) set of sequences.

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CesGO

Description

CeSGO offers a complete Virtual Research Environment (VRE) for Life Sciences. This VRE is based on a collaborative environment built on Wordpress and BuddyPress. It associated to the data sharing services of Owncloud and the SEEK platform.

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Aureme

Description

The toolbox AuReMe allows for the Automatic Reconstruction of Metabolic networks based on the combination
of multiple heteregeneous data and knowledge sources. Since 2016, the workflow has been made available
as a Docker image to facilitate its distribution among the scientific community

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Minia

Description

Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).

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GATB

Description

The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms to analyse NGS datasets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes).

Access conditions

Freely available.

Domains of activity

Biomedical

Agri-food

Environment

Biotechnology

Biology

Description of expertise domains

GenOuest offers many services: 1) a bioinformatics infrastructure: a complete environment for users with or without the support of the core facility members. 2) bioinformatics application development : for the projects requiring software development the coders of the facility bring their expertise to build specific environments or interface of databases. 3) expertise and consulting : GenOuest members can provide help for scientific projects (data analysis, data management plans, etc.) 4) Technological transfer: since the GenOuest core facility is hosted by a computer science institute many tools originating from computer science research can be transferred. 5) Training: many training sessions on tools, environments or methodologies are provided by GenOuest engineers. 6) Scientific hosting : in partnership with GenOuest, users can install or setup new resources to disseminate their research activities.

Besides, GenOuest carries out research and developments in several fields :

These two main fields are federated in a E-science project centered on Virtual Research Environments.

The platform is in close interaction with two local bioinformatics teams, Dyliss and GenScale. The Dyliss team specializes on sequence analysis and systems biology using formal systems to characterize the genetic factors controlling phenotypic responses depending on the environment. The GenScale team focuses on analysis of genomic data on a large scale in developing optimized algorithms (CPU and memory), and which can also be run in parallel environments. The areas of expertise of these two teams contribute to reinforce the expertise of the GenOuest platform and offer innovative tools.

The GenOuest platform is also associated very closely with INRA Bipaa platform which offers resources bioinformatics for Genomics and post-Genomics of insects.

From a thematic point of view, the tools and methodologies developed within this group of fifty people are used in the traditional scientific domains of Biogenouest: sea, agriculture, health and environment.